|
| Status |
Public on Dec 31, 2016 |
| Title |
HFD26 |
| Sample type |
SRA |
| |
|
| Source name |
gastric epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: stomach
cell type: gastric epithelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I. Ribosomal RNA (rRNA) was removed from total RNA using Low Input RiboMinus Eukaryote System v2 (Life Technologies).
RNA-seq libraries were prepared for sequencing using Ion Total RNA-Seq Kit v2 without Barcoding according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using AvadisNGS1.5 Software.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.17.0; tab-delimited text files include RPKM values, count of tags, and total exon length for each gene;
|
| |
|
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
noriko nishi |
| Organization name |
Axiohelix Co. Ltd.
|
| Street address |
5-11 hakozaki 5F Yunibasaru Bldg
|
| City |
tyuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
103-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE67957 |
Transcriptome Analysis of gastric epithelial cells isolated from high fat diet (HFD)-fed mice by using Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN03487358 |
| SRA |
SRX997473 |
